NIE not showing as valid

Good Morning. Has anybody had any issues using their NIE numbers? My brother entered his on a form when purchasing something online a few weeks ago and it said the number wasn't recognised, we assumed it was a fault on the website and he just used mine but yesterday he had a delivery at customs and DHL wanted his NIE and again they said it was coming up so he used mine. Has anyone else had a problem and also where/who would we contact to check and rectify it? He needs to transfer a car into his name so he needs his NIE to be registered correctly. Thank you. Anna